Here are a few areas to investigate further:
- When built-up roofing gets wet and overflows onto light-colored surfaces it looks like rust stains.
- Metal flashing used with built-up roofing and/or your ceramic tile may be rusting. The rust can be passed readily from the metal to the stucco when you wash the deck and when it rains.
- Wood trim or a handrail nailed to the edge of the deck may be the bad guy. Tannic acid in the wood, in reaction with iron in the nails, causes black streaks that might be confused with rust. If this is the case, remove the trim, paint the backside with an oil-base primer, and replace the trim using U.S.-made hot-dipped galvanized nails.
In any case you need to prevent water from carrying dirt and residue from your deck down the walls. The joint at which they meet deserves close attention.
If all this leaves you confused, a home inspector or general repair contractor should be your next step.